Category Archives: Data Review
FreeStyle tutorial: Elemental Composition
The video below demonstrates how to determine the elemental composition of a spectral peak, through annotated click-through text.
FreeStyle tutorial: Displaying Mass Spectra
The video below demonstrates how to mass spectra inside of a workspace, through annotated click-through text.
FreeStyle tutorial: mzVault Searches
The video below demonstrates how to perform mzVault library searches of spectra, through annotated click-through text.
Tip for Optimizing the Speed of Processing Data for TraceFinder 4.0 and later
TraceFinder 4.0 introduced the ability to perform target analysis on peptide sequences. Given that these chemical analysis methods can be very long (i.e. 3hours for a single sample) and have drastically shifting retention times between samples, TF 4.0 introduced the Extraction Time Window as a peak detection setting.
This new setting allows the user to set a window around where the peak might elute. The default setting is 3 minutes, which means +/- 1.5 minutes from the expected retention time.
This setting may be a bit wide for stable chromatography. A typical setting for the Extraction Time Window is 1 minute or +/- 30 seconds from the expected retention time. This setting can be changed in the Master Method Template or the Local Method. This new setting can then be pushed to all the compounds with two mouse clicks or can be optimized for each target peak, clicking the Three Lined Button in the right coner of the settings page and selecting “Apply current extraction window settings to all peaks in the method”
Since the amount of data being extracted for the targeted peak is reduced, the amount of time per peak analysis is reduced. This setting is separate from the Peak Detection and View Width Window under the Retention Times Tab.
Peak Extraction Window
How to use the Threshold Sample in Comparative View
To utilize comparative view to its fullest, one must set 3 three properties.
- Method-Limits-Threshold setting – this setting allows the user to set the height of the horizontal threshold bar in data review. There are two settings.
- Threshold – a fixed peak height amount
- % of Threshold the Sample – dynamic threshold according the peak height of the specified Threshold sample, as described below.
- Batch view-samples-groups column – this setting assigns samples to groups that are displayed horizontally in the comparative view peaks panel. A unique alpha numeric symbol is used to assign a sample to a group. Each sample with the same symbol is a member of that group. The samples are shown side by side in the peak review panel and are ordered left to right by descending order in the sample grid above.
- Batch view-threshold samples – the setting allows the user to assign a threshold sample for each group. Any member of the group can be set as the threshold sample. However, only one sample can be utilized at a time in the group. If you want one particular sample to be used as the threshold across the batch make sure it is a member of all the group. For example if you used numbers for the group name and you have 10 groups, the entry for this sample in the groups column would be 1,2,3,4,5,6,7,8,9,10.
The settings in the examples above allow for the display shown below.
The tall red vertical bar marks the expected retention time and the smaller vertical bars are the edges of the retention time window. Both set in the method parameters for each compound. This allows you to see the drift of chromatography within the sample group. The horizontal red line is the threshold as set in the method as a fixed amount or relative percentage of the threshold sample, as set in the method.
A point to note, there were a few instances where everything was setup properly but nothing displayed in the Comparative view. It was found that some older video drivers not comply with technologies Microsoft used to render the images in this complex grid. However, the issue was fixed in all cases by updating to the latest video drivers for the PC.
TF 3.2 Setting up to Data Review to display Positive results first
In the video below, we have set up the flagging criteria to be able to sort and float Positive results, above the LOR/Cutoff Limit set in the method settings,to the top of the data review grid. We have also setup a flag to allow compounds with detected peaks but fall under the LOR/Cuttoff level in the QAQC section of the master/local method, to appear below the positive results. This should assist in labs wanting to review data by exception and to validate their data review process to incorporate into their SOPs to utilize this criteria.
The Power of Comparing – Do these things go together? – TF 3.1: The NEW Comparative View in Data Review
Many have asked us, how to easily compare compound response across multiple samples.
Here is the answer.
Comparative View allows for a group of samples to be shown side by side with fixed Y-scale to the most intense or a selected threshold reference sample.
The view allows the user to visualize the Expected Retention Time and the Range of Time for peak detection via Markers. This will clearly indicate how the chromatography is responding.
The user can designate samples to be part of individual or multiple groups, by assigning alpha-numeric characters to column in the sample definition screen. Once assigned, and a member of the group is selected in the results grid, the multi-chromatogram pane will display the sample group in columns and the compounds in rows.
The use of a Threshold Sample and a new tab in the method under the Limits section, allows for a visual bar to be set for a specific peak height or a percentage of the Threshold Sample’s peak height.
Below is a video of the new feature in TraceFinder 3.1, debuting at ASMS 2013.
If the video is blurry please click the cog wheel at the bottom of the panel and increase the video display resolution.
Applying an external/historical curve to a batch of samples after Acquisition – Ask A Guru
The video below shows how to apply a calibration curve from one batch that contains calibration samples to a batch of samples that contain no calibrators.
This workflow is the same as selecting the external curve in the Acquisition workflow, but may be used on any batch of samples after acquisition.
The features allows the user to run a calibration batch in the morning and use that curve for all subsequent batches for the time period their SOP allows.
HMMMMMM… Maybe your day just got alittle easier.
If the video is blurry please click the cog wheel at the bottom of the panel and increase the video display resolution.
TF3.0 – Using Estimated/Semi-Quan Amounts
In certain parts of TraceFinder and LabForms, we had exposed the ability to use estimated amounts of substances that did not have their own calibration curve. This feature goes back to the days of the Incos data systems, circa 1980.
In TF 3.0 we have exposed this capability, to be a bit more friendly to use and to be interactive in the user interface, versus just report generated.
In the following video, you will see where to set a compound to use the estimated feature and how it is displayed throughout the applications with visual clues to help you determine that the results you are observing is a semi-quantitative amount.
If the video is blurry please click the cog wheel at the bottom of the panel and increase the video display resolution.
TraceFinder: Direct Knowledge 